LOCUS       NZ_CP041268             1980 bp    DNA     linear   CON 20-APR-2024
DEFINITION  Enterococcus faecium strain VVEswe-R plasmid pVVEswe-R8.
ACCESSION   NZ_CP041268
VERSION     NZ_CP041268.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12138936
            Assembly: GCF_007917035.2
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 1980)
  AUTHORS   Wagner,T.M., Janice,J., Sivertsen,A., Sjogren,I., Sundsfjord,A. and
            Hegstad,K.
  TITLE     Alternative vanHAX promoters and increased vanA-plasmid copy number
            resurrect silenced glycopeptide resistance in Enterococcus faecium
  JOURNAL   J Antimicrob Chemother 76 (4), 876-882 (2021)
   PUBMED   33367710
REFERENCE   2  (bases 1 to 1980)
  AUTHORS   Wagner,T.M., Janice,J., Sivertsen,A., Sjogren,I., Sundsfjord,A. and
            Hegstad,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-MAY-2020) Department of Microbiology and Infection
            Control, Norwegian National Advisory Unit on Detection of
            Antimicrobial Resistance, Sykehusveien 38, Tromso 9038, Norway
  REMARK    Sequence update by submitter
REFERENCE   3  (bases 1 to 1980)
  AUTHORS   Wagner,T.M., Janice,J., Sivertsen,A., Sjogren,I., Sundsfjord,A. and
            Hegstad,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-JUN-2019) Department of Microbiology and Infection
            Control, Norwegian National Advisory Unit on Detection of
            Antimicrobial Resistance, Sykehusveien 38, Tromso 9038, Norway
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2019
            Assembly Method                   :: Unicycler v. v0.4.6
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 305.0x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_007917035.2-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 02:37:42
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,257
            CDSs (total)                      :: 3,164
            Genes (coding)                    :: 3,041
            CDSs (with protein)               :: 3,041
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 58 of 123
            Pseudo Genes (incomplete)         :: 63 of 123
            Pseudo Genes (internal stop)      :: 24 of 123
            Pseudo Genes (multiple problems)  :: 18 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041268.2.
            On Jun 19, 2020 this sequence version replaced NZ_CP041268.1.
            Bacteria and source DNA available from KRES.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..1980
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="VVEswe-R"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pVVEswe-R8"
                     /geo_loc_name="Sweden:Halmstad"
                     /lat_lon="56.6744 N 12.8578 E"
                     /collection_date="2014"
                     /collected_by="KRES"
     gene            complement(204..1220)
                     /locus_tag="FKW92_RS15920"
                     /old_locus_tag="FKW92_16785"
     CDS             complement(204..1220)
                     /locus_tag="FKW92_RS15920"
                     /old_locus_tag="FKW92_16785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002299382.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003916 - DNA topoisomerase activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation factor domain-containing
                     protein"
                     /protein_id="WP_002326787.1"
                     /translation="MANENQLSEIQSKIEGRGAEKRTTINQLEKLNRISNRRLSVDDKV
                     HPLKLSWSIDRITIVGKLNDTIAYWTQNGVVFVDFEQLMRLNENQGYLKSVGTNGWQLF
                     DQYGEDIAYIEMLKFHPDKGRIDFNPNKIGEFLKGSMKQFIHDLFLDAHFSRADIACDI
                     LGVPDDFITQYRIVDPVSFKPIYGRSGKLETAYWGSRASERQVRMYNKKLEQERKKQIV
                     PKEIETWWRIEMQLRRGKATDWHAMVRESLDSFASPHYLPGDVKPVDRIMIKGLNQDHS
                     EWAYISRNLKYRLRKLLKEESQNDELTNHLRETFKESANDLKIELDTWLLGLDVTEK"
                     /name="replication initiation factor domain-containing
                     protein"
     gene            complement(1780..>1980)
                     /locus_tag="FKW92_RS16170"
     CDS             complement(1780..>1980)
                     /locus_tag="FKW92_RS16170"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_217510307.1"
                     /translation="SQLGKCYSLSKSNRKVYTLFISDSAKEGFNLGFSISFKKGTKNTS
                     ISHNNRELTDSQKINGLSGRK"
                     /name="hypothetical protein"
     Typing          complement(205..971)
                     /name="rep_cluster_1968"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcatggctgt cacaattcca aatgctctcc gagggtattc gctgtcacaa gtgacaacga
       61 aaaaaggagc cgaaagcgtg tcacgctctc aactcctttt acgctttatt ttgcttcacg
      121 caaaataatc gcttatcgta aactcacgtc attaaacatt gacgtaaatt tactctcact
      181 catctgactt ttcttattcg gtatcacttc tctgtcacgt ccaaacccaa aagccacgtg
      241 tctaattcta ttttcaagtc gtttgcagat tccttaaacg tctctcgtaa atgattcgtc
      301 aactcatcgt tttggctttc ttctttcaac aatttgcgca atctatattt caaatttctg
      361 ctaatatacg cccactctga atgatcttga ttcagccctt ttatcataat tctatcaaca
      421 ggttttacat ctccaggcaa gtaatgagga cttgcaaagc tatctaaact ttcccgaacc
      481 atcgcatgcc aatctgttgc tttgccacgt cttagctgca tttctatacg ccaccatgtt
      541 tcgatttctt ttggtacaat ctgttttttt cgttcctgtt caagcttttt gttgtacatc
      601 cgcacttgtc gctcgctggc acgactaccc cagtacgctg tttctaattt gccagaacgg
      661 ccataaattg gcttaaaaga cacagggtca acgattcgat actgggtaat aaaatcatca
      721 ggaacaccga gaatatcgca agcaatatct gcacgtgaga aatgcgcatc cagaaacaaa
      781 tcatgaatga attgtttcat cgaccccttt aaaaactcgc caattttatt tggattaaaa
      841 tcaatacgac ctttgtcagg gtgaaatttt aacatttcga tataggcgat atcttctcca
      901 tattggtcaa ataattgcca accatttgta ccaaccgact tcaaataccc ttgattttca
      961 ttcaaacgca ttaattgctc aaaatcgaca aacacaactc cattttgcgt ccaataagct
     1021 atggtatcat tcagttttcc gacgattgta attcgatcga ttgaccaact taattttagg
     1081 gggtgtacct tatcgtcaac acttaaccgc ctgttagaaa tacggttaag tttttcgagc
     1141 tgatttatcg ttgttctttt ttctgcccct cgaccttcaa tttttgattg aatttcactc
     1201 aactgatttt catttgccat tttcgtcctc cagacgaaaa aagagacttt tggaaagaat
     1261 ttccagagtt cacgtaaccc taaaaattca tatccaaaaa tctctagctt gaagaaacct
     1321 aaaaatattc gtataatgaa cctgagttac ggagctaggt gaagtagttt ccgtaaatag
     1381 tcgagagtgt tagcgcactg ctcggctttt attttgctct tttttctcgt tttctttgat
     1441 tatagcactc ctcctaaaaa aataaaaaga cctcagggaa tttcattccc cgaacccctt
     1501 gagcctcctc ctgccgaaat ggaaagggcg cacccgctgt ttatttcatt cagctatcgg
     1561 ttttcacaat ctaacacgat cgttccgcta ccagtcgcct tacaggctcc attttcgctc
     1621 ctctaacgtg ttttaacgat tgtgccgata actaaacgaa ataaacgcta aaaccgctca
     1681 gaacgcaaaa tatgccattt tagagctatt gtagaaaatg tagtttgaaa tgcaattttc
     1741 ttctttcagc tttttatttc ccacttgtaa atctgctaat tattttctac cagacaaacc
     1801 attgattttt tggctatcag ttaactcacg attattatga gaaatgcttg tattctttgt
     1861 tccctttttg aacgaaatac taaaccccaa gttaaacccc tccttcgcgc tgtcgctaat
     1921 aaaaagagtg taaacctttc tgttactctt tgacaaagag taacattttc ctaattgtga
//
